The Sha’arei Teshuva at the end of O.C. 495 quotes a machlokes achronim whether a kohen who comes to chutz la’aretz from Eretz Yisrael to visit and therefore observes only one day of Yom Tov can go up to duchen on Yom Tov sheni. At first glance the safeik seems a bit hard to understand. I can understand why achronim might debate issues like what tefilah a ben Eretz Yisrael visiting chu”l should say on Y”Y sheni, as the tefilos of chu”l on Yom Tov are completely different than what a ben Eretz Yisrael would daven if he were home. However, when it comes to duchening, the minhag in Eretz Yisrael is to duchen every day anyway. M’mah nafshach: if the kohen follows minhag Eretz Yisrael, he should duchen; if he follows minhag chu”l and it is Yom Tov, he should also duchen – so what’s the safeik?
I think we see from here proof to a yesod that the Rav has in Shiurim l’Zecher Aba Mori that there are 2 dinim in birchas kohanim: 1) an independent mitzvah; 2) part of the cheftza of tefilah.
There is an interesting Yersuahlmi at the beginning of the 4th perek of Ta’anis:
מניין לנשיאות כפים (במדבר ו) כה תברכו את בני ישראל. עד כאן בשחרית במוסף (ויקרא ט) וישא אהרן את ידיו אל העם.
The Yerushalmi actually has two separate sources for birchas kohanim, one from parshas Naso, one from our parsha (Shmini) where birchas kohanim (see Rashi, Ramban) is mentioned as a concluding element of Aharon’s avodah. These two sources may reflect these two dimensions of the mitzvah. The chiddush of our parsha and the reason that we situate birchas kohanim in “retzeih” is because birchas kohanim must take place in the context of avodah/tefilah.
The Gilyon on the Yerushalmi at the beginning of that perek reflects the same idea. He is mechadesh that the reason we do not do birchas kohanim at night is not because avodah is never done at night, but rather it is because tefilas arvis reshus – we do not have a formal obligation of tefilah at night and therefore birchas kohanim has no context.
Returning to our issue, since a kohen who is a ben Eretz Yisrael would not daven a tefilas musaf on Yom Tov sheni, he lacks a cheftza shel tefilah in which to incorporate birchas kohanim (note that the second source quoted by the Yerushalmi addresses itself specifically to musaf!) and is therefore exempt from the mitzvah.